getRefRun: Fetch the reference run for each peptide

In shubham1637/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

Fetch the reference run for each peptide

Description

Provides the reference run based on lowest p-value.

Usage

getRefRun(peptideScores, applyFun = lapply)

Arguments

peptideScores	(list of data-frames) each dataframe has scores of a peptide across all runs.
applyFun	(function) value must be either lapply or BiocParallel::bplapply.

Value

(dataframe) has two columns:

peptide_id	(integer) a unique id for each peptide.
run	(string) run identifier.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-04-08

See Also

getPeptideScores

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- getRunNames(dataPath = dataPath)
precursorsInfo <- getPrecursors(fileInfo, oswMerged = TRUE, runType = "DIA_Proteomics",
                                context = "experiment-wide", maxPeptideFdr = 0.05)
peptideIDs <- unique(precursorsInfo$peptide_id)
peptidesInfo <- getPeptideScores(fileInfo, peptideIDs)
peptidesInfo <- lapply(peptideIDs, function(pep) peptidesInfo [.(pep),])
names(peptidesInfo) <- as.character(peptideIDs)
getRefRun(peptidesInfo)

shubham1637/DIAlign documentation built on March 27, 2023, 7:12 a.m.